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- PDB-4gun: Crystal Structure of the K184R, L185P mutant manganese superoxide... -

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Basic information

Entry
Database: PDB / ID: 4gun
TitleCrystal Structure of the K184R, L185P mutant manganese superoxide dismutase from Candida albicans cytosol
ComponentsSuperoxide dismutase
KeywordsOXIDOREDUCTASE / Mn Superoxide Dismutase
Function / homology
Function and homology information


superoxide dismutase / superoxide dismutase activity / metal ion binding
Similarity search - Function
Iron/manganese superoxide dismutase, C-terminal domain / Fe,Mn superoxide dismutase (SOD) domain / minor pseudopilin epsh fold / 3-Layer(bab) Sandwich / Manganese/iron superoxide dismutase, binding site / Manganese and iron superoxide dismutases signature. / Manganese/iron superoxide dismutase / Manganese/iron superoxide dismutase, N-terminal / Iron/manganese superoxide dismutases, alpha-hairpin domain / Manganese/iron superoxide dismutase, C-terminal ...Iron/manganese superoxide dismutase, C-terminal domain / Fe,Mn superoxide dismutase (SOD) domain / minor pseudopilin epsh fold / 3-Layer(bab) Sandwich / Manganese/iron superoxide dismutase, binding site / Manganese and iron superoxide dismutases signature. / Manganese/iron superoxide dismutase / Manganese/iron superoxide dismutase, N-terminal / Iron/manganese superoxide dismutases, alpha-hairpin domain / Manganese/iron superoxide dismutase, C-terminal / Manganese/iron superoxide dismutase, C-terminal domain superfamily / Iron/manganese superoxide dismutases, C-terminal domain / Manganese/iron superoxide dismutase, N-terminal domain superfamily / Helix Hairpins / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / Superoxide dismutase
Similarity search - Component
Biological speciesCandida albicans (yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.94 Å
AuthorsSheng, Y. / Cascio, D. / Valentine, J.S.
CitationJournal: TO BE PUBLISHED
Title: Crystal Structure of the K184R, L185P mutant manganese superoxide dismutase from Candida albicans cytosol
Authors: Sheng, Y. / Cascio, D. / Valentine, J.S.
History
DepositionAug 29, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Superoxide dismutase
B: Superoxide dismutase
C: Superoxide dismutase
D: Superoxide dismutase
E: Superoxide dismutase
F: Superoxide dismutase
G: Superoxide dismutase
H: Superoxide dismutase
I: Superoxide dismutase
J: Superoxide dismutase
K: Superoxide dismutase
L: Superoxide dismutase
M: Superoxide dismutase
N: Superoxide dismutase
O: Superoxide dismutase
P: Superoxide dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)367,75558
Polymers364,37816
Non-polymers3,37742
Water18,8981049
1
A: Superoxide dismutase
B: Superoxide dismutase
C: Superoxide dismutase
D: Superoxide dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,89114
Polymers91,0954
Non-polymers79610
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10240 Å2
ΔGint-42 kcal/mol
Surface area30710 Å2
MethodPISA
2
E: Superoxide dismutase
F: Superoxide dismutase
G: Superoxide dismutase
H: Superoxide dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,08316
Polymers91,0954
Non-polymers98812
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10250 Å2
ΔGint-46 kcal/mol
Surface area30650 Å2
MethodPISA
3
I: Superoxide dismutase
J: Superoxide dismutase
K: Superoxide dismutase
L: Superoxide dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,98715
Polymers91,0954
Non-polymers89211
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10290 Å2
ΔGint-43 kcal/mol
Surface area30700 Å2
MethodPISA
4
M: Superoxide dismutase
N: Superoxide dismutase
O: Superoxide dismutase
P: Superoxide dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,79513
Polymers91,0954
Non-polymers7009
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10280 Å2
ΔGint-44 kcal/mol
Surface area30770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.330, 73.800, 134.290
Angle α, β, γ (deg.)90.000, 109.300, 90.000
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Superoxide dismutase /


Mass: 22773.635 Da / Num. of mol.: 16 / Mutation: K184R, L185P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida albicans (yeast) / Gene: CaJ7.0018, SOD3 / Plasmid: pVT102U / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): EG110 / References: UniProt: Q96UT6, superoxide dismutase
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Mn
#3: Chemical...
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 26 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1049 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.32 Å3/Da / Density % sol: 62.95 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2 M ammonium sulfate, pH 7.0, vapor diffusion, hanging drop, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Nov 10, 2011
RadiationMonochromator: CONFOCAL MIRRORS Varimax HF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.94→53.02 Å / Num. obs: 314901 / % possible obs: 91.3 % / Observed criterion σ(I): -3 / Redundancy: 3.83 % / Biso Wilson estimate: 21.652 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 9.94
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.94-1.990.2953.21459471647164.4
1.99-2.050.2674.44847192227989.6
2.05-2.110.2265.26882652221891.9
2.11-2.170.1936.04863092171092.3
2.17-2.240.2055.9791792008188.2
2.24-2.320.177.72749721949488.4
2.32-2.410.1587.13787001982593.6
2.41-2.510.1328.26761391923493.9
2.51-2.620.1238.67732601854394.3
2.62-2.750.1149.28700811776294.7
2.75-2.90.09111.24664231693595.2
2.9-3.070.08312.4631981617695.5
3.07-3.290.06914.05584171510895.8
3.29-3.550.06315.56546181423996.2
3.55-3.890.0617.17476481277294.2
3.89-4.350.05118.89449081192996.7
4.35-5.020.0519.13394191046897.4
5.02-6.150.05317.1634151898197.8
6.15-8.690.04918.3126057690298
8.690.03922.213813377497.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å53.02 Å
Translation2.5 Å53.02 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.3.0phasing
BUSTER-TNTrefinement
PDB_EXTRACT3.11data extraction
CrystalCleardata collection
XDSdata reduction
BUSTER2.10.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QVN

3qvn


Resolution: 1.94→53.02 Å / Cor.coef. Fo:Fc: 0.8994 / Cor.coef. Fo:Fc free: 0.8764 / Occupancy max: 1 / Occupancy min: 0.45 / SU R Cruickshank DPI: 0.171 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2657 15957 5.07 %RANDOM
Rwork0.238 ---
obs0.2394 314899 90.76 %-
Displacement parametersBiso max: 95.11 Å2 / Biso mean: 16.3786 Å2 / Biso min: 3 Å2
Baniso -1Baniso -2Baniso -3
1--8.3231 Å20.0815 Å2-4.5833 Å2
2--6.4604 Å2-0.1171 Å2
3---1.8627 Å2
Refine analyzeLuzzati coordinate error obs: 0.302 Å
Refinement stepCycle: LAST / Resolution: 1.94→53.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25448 0 146 1049 26643
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d8633SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes727HARMONIC2
X-RAY DIFFRACTIONt_gen_planes3773HARMONIC5
X-RAY DIFFRACTIONt_it26234HARMONIC20
X-RAY DIFFRACTIONt_nbd16SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion3477SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact31520SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d26234HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg35799HARMONIC21.08
X-RAY DIFFRACTIONt_omega_torsion3.11
X-RAY DIFFRACTIONt_other_torsion17.26
LS refinement shellResolution: 1.94→1.99 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2736 758 5.08 %
Rwork0.2351 14160 -
all0.237 14918 -
obs--90.76 %

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